Chiphead,
OK here we go. 1st thing is to find machinist that will work the way you say!!!! Then take your mics and standards and compare them to his. Another thing is to keep the temp pretty constant when you measure anything. Your machinist should be able to advise you as to what size bore you can use, order up your pistons before he bores it. Then discuss what kind of piston to wall clearance you want to run. He can then clean the bores to that dimension. Unless you are going to run something exotic I would forego line boring the mains. Discuss how much the crank will need to be ground. Then order up the appropriate bearings and torque them into your block and measure them. Give your measurements to the machinist. As far as thrust measurements, I would kinda wing it by measuring it with the old stuff in it and then comparing the new thrust bearing against the old. Number all the rods and caps so they can go back in the same. Have the rods rebuilt. Have the machinist install the cam bearings as the tools are not worth having unless you're gonna make a carreer of this. Be sure to check that the oil holes are lined up on the cam bearings. Static balance the piston/rod assembly. Dynamically balance the crank, damper, flywheel/pressure plate seperately. I'm tired of typing now. If you need the top end stuff It'll have to wait for another day.
Regards
Dennis